Commercial electrodes used for Deep Brain Stimulation (DBS) cause severe artefacts in conventional echo based MRI. Here we show near artefact free functional MRI during DBS in rats using Multi-Band SWeep Imaging with Fourier Transformation (MB-SWIFT) which allows acquisition at virtually zero-TE. MB-SWIFT showed strong responses in the somatosensory cortex while stimulating the ventromedial. The amplitude and extent of activation recorded with MB-SWIFT were similar with SE-EPI, although activation was flip angle dependent reflecting the possible influence of blood inflow. MB-SWIFT is a promising modality for fMRI in the presence of DBS leads or other severe susceptibility differences.